A distinct QscR regulon in the Pseudomonas aeruginosa quorum-sensing circuit

Abstract

The opportunistic pathogen Pseudomonas aeruginosa possesses two complete acyl-homoserine lactone (acyl-HSL) signaling systems. One system consists of LasI and LasR, which generate a 3-oxododecanoyl-homoserine lactone signal and respond to that signal, respectively. The other system is RhlI and RhlR, which generate butanoyl-homoserine lactone and respond to butanoyl-homoserine lactone, respectively. These quorum-sensing systems control hundreds of genes. There is also an orphan LasR-RhlR homolog, QscR, for which there is no cognate acyl-HSL synthetic enzyme. We previously reported that a qscR mutant is hypervirulent and showed that QscR transiently represses a few quorum-sensing-controlled genes. To better understand the role of QscR in P. aeruginosa gene regulation and to better understand the relationship between QscR, LasR, and RhlR control of gene expression, we used transcription profiling to identify a QscR-dependent regulon. Our analysis revealed that QscR activates some genes and represses others. Some of the repressed genes are not regulated by the LasR-I or RhlR-I systems, while others are. The LasI-generated 3-oxododecanoyl-homoserine lactone serves as a signal molecule for QscR. Thus, QscR appears to be an integral component of the P. aeruginosa quorum-sensing circuitry. QscR uses the LasI-generated acyl-homoserine lactone signal and controls a specific regulon that overlaps with the already overlapping LasR- and RhlR-dependent regulons.

FIG. 1.

GeneSpring cluster analysis of P. aeruginosa QscR-regulated genes and examples of transcript levels for members of each class of expression pattern at different culture densities. (A) Cluster analysis. Red indicates negative changes in transcript levels of the parent compared to the qscR null mutant, and green indicates positive changes in transcript levels of the parent compared to the qscR null mutant. Class I, genes regulated in logarithmic phase; class II, genes regulated during the transition from logarithmic to stationary phase; class III, genes regulated in stationary phase; class IV, genes regulated throughout growth; class V, genes discontinuously regulated. (B) Transcript levels (×1,000; units as determined by array software) for representative members of each class. Transcript levels of the qscR null mutant (○) and wild type (▿) are shown. The gene numbers or gene names are indicated according to the Pseudomonas Genome Project website (http://www.pseudomonas.com).

FIG. 2.

Transcript levels of PA1897-1894 in the P. aeruginosa parent strain and in P. aeruginosa qscR mutants. The qscR mutants are the qscR null mutant, the strain expressing l-arabinose promoter-driven qscR (pbad-qscR), and the strain expressing the l-arabinose promoter-driven qscR deletion that codes for a polypeptide with a truncation of the C-terminal DNA-binding domain (pbad-qscR-Δdbd). Transcript levels from cultures at an optical density (600 nm) of 1.4 are the averages of transcript levels for PA1897, PA1895, and PA1894 open reading frames from our microarray data. Errors bars show the standard deviations.

FIG. 3.

Venn diagrams showing overlaps between QscR-repressed and QscR-activated genes and LasR-I and RhlR-I regulons. Blue, genes that require LasR-I for activation; yellow, genes that require RhlR-I for activation; gray, genes that require both LasR-I and RhlR-I for activation. (A) Green, QscR-activated genes. (B) Pink, QscR-repressed genes. There are an additional 274 QscR-dependent genes that are not induced by the LasR-I or RhlR-I systems and are not represented in these Venn diagrams.